void MuscleOutput(MSA &msa) { MHackEnd(msa); if (g_bStable) { MSA msaStable; Stabilize(msa, msaStable); msa.Clear(); // save memory DoOutput(msaStable); } else DoOutput(msa); }
void prepareAlignResults(MSA& msa, const DNAAlphabet* al, MultipleSequenceAlignment& ma, bool mhack) { if (mhack) { MHackEnd(msa); } MuscleContext* ctx = getMuscleContext(); if (ctx->params.g_bStable) { MSA msaStable; Stabilize(msa, msaStable); msa.Clear(); convertMSA2MAlignment(msaStable, al, ma); } else { convertMSA2MAlignment(msa, al, ma); } }
void ProgAlignSubFams() { MSA msaOut; SetOutputFileName(g_pstrOutFileName.get()); SetInputFileName(g_pstrInFileName.get()); SetMaxIters(g_uMaxIters.get()); SetSeqWeightMethod(g_SeqWeight1.get()); TextFile fileIn(g_pstrInFileName.get()); SeqVect v; v.FromFASTAFile(fileIn); const unsigned uSeqCount = v.Length(); if (0 == uSeqCount) Quit("No sequences in input file"); ALPHA Alpha = ALPHA_Undefined; switch (g_SeqType.get()) { case SEQTYPE_Auto: Alpha = v.GuessAlpha(); break; case SEQTYPE_Protein: Alpha = ALPHA_Amino; break; case SEQTYPE_DNA: Alpha = ALPHA_DNA; break; case SEQTYPE_RNA: Alpha = ALPHA_RNA; break; default: Quit("Invalid seq type"); } SetAlpha(Alpha); v.FixAlpha(); PTR_SCOREMATRIX UserMatrix = 0; if (0 != g_pstrMatrixFileName.get()) { const char *FileName = g_pstrMatrixFileName.get(); const char *Path = getenv("MUSCLE_MXPATH"); if (Path != 0) { size_t n = strlen(Path) + 1 + strlen(FileName) + 1; char *NewFileName = new char[n]; sprintf(NewFileName, "%s/%s", Path, FileName); FileName = NewFileName; } TextFile File(FileName); UserMatrix = ReadMx(File); g_Alpha = ALPHA_Amino; g_PPScore = PPSCORE_SP; } SetPPScore(); if (0 != UserMatrix) g_ptrScoreMatrix = UserMatrix; if (ALPHA_DNA == Alpha || ALPHA_RNA == Alpha) { SetPPScore(PPSCORE_SPN); g_Distance1.get() = DISTANCE_Kmer4_6; } unsigned uMaxL = 0; unsigned uTotL = 0; for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) { unsigned L = v.GetSeq(uSeqIndex).Length(); uTotL += L; if (L > uMaxL) uMaxL = L; } SetIter(1); g_bDiags.get() = g_bDiags1.get(); SetSeqStats(uSeqCount, uMaxL, uTotL/uSeqCount); SetMuscleSeqVect(v); MSA::SetIdCount(uSeqCount); // Initialize sequence ids. // From this point on, ids must somehow propogate from here. for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex) v.SetSeqId(uSeqIndex, uSeqIndex); if (uSeqCount > 1) MHackStart(v); if (0 == uSeqCount) { msaOut.Clear(); return; } if (1 == uSeqCount && ALPHA_Amino == Alpha) { const Seq &s = v.GetSeq(0); msaOut.FromSeq(s); return; } Tree GuideTree; TreeFromSeqVect(v, GuideTree, g_Cluster1.get(), g_Distance1.get(), g_Root1.get()); SetMuscleTree(GuideTree); MSA msa; if (g_bLow.get()) { ProgNode *ProgNodes = 0; ProgNodes = ProgressiveAlignE(v, GuideTree, msa); delete[] ProgNodes; } else ProgressiveAlign(v, GuideTree, msa); SetCurrentAlignment(msa); TreeFromMSA(msa, GuideTree, g_Cluster2.get(), g_Distance2.get(), g_Root2.get()); SetMuscleTree(GuideTree); unsigned *SubFams = new unsigned[uSeqCount]; unsigned uSubFamCount; SubFam(GuideTree, g_uMaxSubFamCount.get(), SubFams, &uSubFamCount); SetProgressDesc("Align node"); const unsigned uNodeCount = 2*uSeqCount - 1; ProgNode *ProgNodes = new ProgNode[uNodeCount]; bool *NodeIsSubFam = new bool[uNodeCount]; bool *NodeInSubFam = new bool[uNodeCount]; for (unsigned i = 0; i < uNodeCount; ++i) { NodeIsSubFam[i] = false; NodeInSubFam[i] = false; } for (unsigned i = 0; i < uSubFamCount; ++i) { unsigned uNodeIndex = SubFams[i]; assert(uNodeIndex < uNodeCount); NodeIsSubFam[uNodeIndex] = true; SetInFam(GuideTree, uNodeIndex, NodeInSubFam); } unsigned uJoin = 0; unsigned uTreeNodeIndex = GuideTree.FirstDepthFirstNode(); do { if (NodeIsSubFam[uTreeNodeIndex]) { #if TRACE Log("Node %d: align subfam\n", uTreeNodeIndex); #endif ProgNode &Node = ProgNodes[uTreeNodeIndex]; AlignSubFam(v, GuideTree, uTreeNodeIndex, Node.m_MSA); Node.m_uLength = Node.m_MSA.GetColCount(); } else if (!NodeInSubFam[uTreeNodeIndex]) { #if TRACE Log("Node %d: align two subfams\n", uTreeNodeIndex); #endif Progress(uJoin, uSubFamCount - 1); ++uJoin; const unsigned uMergeNodeIndex = uTreeNodeIndex; ProgNode &Parent = ProgNodes[uMergeNodeIndex]; const unsigned uLeft = GuideTree.GetLeft(uTreeNodeIndex); const unsigned uRight = GuideTree.GetRight(uTreeNodeIndex); ProgNode &Node1 = ProgNodes[uLeft]; ProgNode &Node2 = ProgNodes[uRight]; PWPath Path; AlignTwoMSAs(Node1.m_MSA, Node2.m_MSA, Parent.m_MSA, Path); Parent.m_uLength = Parent.m_MSA.GetColCount(); Node1.m_MSA.Clear(); Node2.m_MSA.Clear(); } else { #if TRACE Log("Node %d: in subfam\n", uTreeNodeIndex); #endif ; } uTreeNodeIndex = GuideTree.NextDepthFirstNode(uTreeNodeIndex); } while (NULL_NEIGHBOR != uTreeNodeIndex); ProgressStepsDone(); unsigned uRootNodeIndex = GuideTree.GetRootNodeIndex(); ProgNode &RootProgNode = ProgNodes[uRootNodeIndex]; TextFile fOut(g_pstrOutFileName.get(), true); MHackEnd(RootProgNode.m_MSA); RootProgNode.m_MSA.ToFile(fOut); delete[] NodeInSubFam; delete[] NodeIsSubFam; delete[] ProgNodes; delete[] SubFams; ProgNodes = 0; NodeInSubFam = 0; NodeIsSubFam = 0; SubFams = 0; }